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Foods
Special Issues
Advances in Foodborne Pathogen Analysis and Detection
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Advances in Foodborne Pathogen Analysis and Detection

A special issue of Foods (ISSN 2304-8158). This special issue belongs to the section "Food Analytical Methods".

Deadline for manuscript submissions: 31 March 2025 | Viewed by 3151

Special Issue Editors

Dr. Andrew G. Gehring

E-Mail Website
Guest Editor
Characterization and Interventions for Foodborne Pathogens, United States Department of Agriculture, Agricultural Research Service, Wyndmoor, PA 19038, USA
Interests: biosensors; food safety; immunoassays; nanopore sequencing; phage typing; rapid methods; sample preparation
Special Issues, Collections and Topics in MDPI journals
Dr. Katrina Counihan

E-Mail Website
Guest Editor Assistant
Characterization and Interventions for Foodborne Pathogens, United States Department of Agriculture, Agricultural Research Service, Wyndmoor, PA 19038, USA
Interests: microbiology; rapid methods; food safety; foodborne pathogens; long-read sequencing

Special Issue Information

Dear Colleagues,

Foodborne pathogens are a major source of illness and an economic burden worldwide. Methods for detecting pathogens in food are vital for protecting consumer health from contaminated products. Current culture-based methods take days to weeks to complete; therefore, there is a need to develop novel methods or improve upon current methods to increase the rapidity of pathogen identification. This Special Issue will focus on the research being conducted to advance any stage of method development, including to suitably prepare food samples for detection, identify pathogens more quickly, detect live versus dead organisms, quantify pathogen presence in a food matrix, and/or establish culture-independent methods. The innovative work being conducted by researchers such as yourself can revolutionize the field of foodborne pathogen detection and reduce the incidence of foodborne disease.

We welcome original and review papers to be included in this Special Issue of Foods. Manuscripts will focus on the following areas: development of new methods or improvement of current methods to screen for the presence of or identify foodborne pathogens more rapidly, novel methods for detecting viable pathogens, novel methods for quantifying pathogens, and/or the development of culture-independent pathogen detection methods.

Dr. Andrew G. Gehring
Guest Editor

Dr. Katrina Counihan
Guest Editor Assistant

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Foods is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • automation
  • confirmation
  • detection
  • foodborne pathogens
  • food safety
  • identification
  • rapid methods
  • sample preparation
  • serotype determination
  • quantification
  • viability
  • zero tolerance

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Further information on MDPI's Special Issue polices can be found here.

Published Papers (3 papers)

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Research

12 pages, 1797 KiB  
Article
Investigating the Quantification Capabilities of a Nanopore-Based Sequencing Platform for Food Safety Application via External Standards of Lambda DNA and Lambda Spiked Beef
by Sky Harper, Katrina L. Counihan, Siddhartha Kanrar, George C. Paoli, Shannon Tilman and Andrew G. Gehring
Foods 2024, 13(20), 3304; https://doi.org/10.3390/foods13203304 - 18 Oct 2024
Viewed by 881
Abstract
Six hundred million cases of disease and roughly 420,000 deaths occur globally each year due to foodborne pathogens. Current methods to screen and identify pathogens in swine, poultry, and cattle products include immuno-based techniques (e.g., immunoassay integrated biosensors), molecular methods (e.g., DNA hybridization [...] Read more.
Six hundred million cases of disease and roughly 420,000 deaths occur globally each year due to foodborne pathogens. Current methods to screen and identify pathogens in swine, poultry, and cattle products include immuno-based techniques (e.g., immunoassay integrated biosensors), molecular methods (e.g., DNA hybridization and PCR assays), and traditional culturing. These methods are often used in tandem to screen, quantify, and characterize samples, prolonging real-time comprehensive analysis. Next-generation sequencing (NGS) is a relatively new technology that combines DNA-sequencing chemistry and bioinformatics to generate and analyze large amounts of short- or long-read DNA sequences and whole genomes. The goal of this project was to evaluate the quantitative capabilities of the real-time NGS Oxford Nanopore Technologies’ MinION sequencer through a shotgun-based sequencing approach. This investigation explored the correlation between known amounts of the analyte (lambda DNA as a pathogenic bacterial surrogate) with data output, in both the presence and absence of a background matrix (Bos taurus DNA). A positive linear correlation was observed between the concentration of analyte and the amount of data produced, number of bases sequenced, and number of reads generated in both the presence and absence of a background matrix. In the presence of bovine DNA, the sequenced data were successfully mapped to the NCBI lambda reference genome. Furthermore, the workflow from pre-extracted DNA to target identification took less than 3 h, demonstrating the potential of long-read sequencing in food safety as a rapid method for screening, identification, and quantification. Full article
(This article belongs to the Special Issue Advances in Foodborne Pathogen Analysis and Detection)
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22 pages, 2684 KiB  
Article
Aggregative Swab Sampling Method for Romaine Lettuce Show Similar Quality and Safety Indicators and Microbial Profiles Compared to Composite Produce Leaf Samples in a Pilot Study
by Rachel J. Gathman, Jorge Quintanilla Portillo, Gustavo A. Reyes, Genevieve Sullivan and Matthew J. Stasiewicz
Foods 2024, 13(19), 3080; https://doi.org/10.3390/foods13193080 - 27 Sep 2024
Viewed by 723
Abstract
Composite produce leaf samples from commercial production rarely test positive for pathogens, potentially due to low pathogen prevalence or the relatively small number of plants sampled. Aggregative sampling may offer a more representative alternative. This pilot study investigated whether aggregative swab samples performed [...] Read more.
Composite produce leaf samples from commercial production rarely test positive for pathogens, potentially due to low pathogen prevalence or the relatively small number of plants sampled. Aggregative sampling may offer a more representative alternative. This pilot study investigated whether aggregative swab samples performed similarly to produce leaf samples in their ability to recover quality indicators (APCs and coliforms), detect Escherichia coli, and recover representative microbial profiles. Aggregative swabs of the outer leaves of romaine plants (n = 12) and composite samples consisting of various grabs of produce leaves (n = 14) were collected from 60 by 28 ft sections of a one-acre commercial romaine lettuce field. Aerobic plate counts were 9.17 ± 0.43 and 9.21 ± 0.42 log(CFU/g) for produce leaf samples and swabs, respectively. Means and variance were not significantly different (p = 0.38 and p = 0.92, respectively). Coliform recoveries were 3.80 ± 0.76 and 4.19 ± 1.15 log(CFU/g) for produce leaf and swabs, respectively. Means and variances were not significantly different (p = 0.30 and p = 0.16, respectively). Swabs detected generic E. coli in 8 of 12 samples, more often than produce leaf samples (3 of 14 positive, Fisher’s p = 0.045). Full-length 16S rRNA microbial profiling revealed that swab and produce leaf samples did not show significantly different alpha diversities (p = 0.75) and had many of the most prevalent bacterial taxa in common and in similar abundances. These data suggest that aggregative swabs perform similarly to, if not better than, produce leaf samples in recovering indicators of quality (aerobic and coliform bacteria) and food safety (E. coli), justifying further method development and validation. Full article
(This article belongs to the Special Issue Advances in Foodborne Pathogen Analysis and Detection)
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14 pages, 2123 KiB  
Article
Evaluating Commercial Loop-Mediated Isothermal Amplification Master Mixes for Enhanced Detection of Foodborne Pathogens
by Ana Costa-Ribeiro, Alexandre Lamas and Alejandro Garrido-Maestu
Foods 2024, 13(11), 1635; https://doi.org/10.3390/foods13111635 - 24 May 2024
Cited by 1 | Viewed by 1084
Abstract
Loop-mediated isothermal amplification, LAMP, is nowadays the most popular isothermal nucleic acid amplification technique, and as such, several commercial, ready-to-use master mixes have flourished. Unfortunately, independent studies to determine their performance are limited. The current study performed an independent evaluation of the existing [...] Read more.
Loop-mediated isothermal amplification, LAMP, is nowadays the most popular isothermal nucleic acid amplification technique, and as such, several commercial, ready-to-use master mixes have flourished. Unfortunately, independent studies to determine their performance are limited. The current study performed an independent evaluation of the existing ready-to-use commercial LAMP master mixes WarmStart® LAMP Kit, LavaLAMP™ DNA Master Mix, Saphir Bst Turbo GreenMaster, OptiGene Fast Master Mix ISO-004, and SynLAMP Mix. To reduce bias, three different genes, namely ttr (Salmonella spp.), rfbE (E. coli O157), and hly (Listeria monocytogenes), were targeted. The comparison was based on amplification speed, performance with decreasing DNA concentrations, and the effect of five typical LAMP reaction additives (betaine, DMSO, pullulan, TMAC, and GuHCl). Significant differences were observed among the different master mixes. OptiGene provided the fastest amplification and showed less detrimental effects associated with the supplements evaluated. Out of the chemicals tested, pullulan provided the best results in terms of amplification speed. It is noteworthy that the different additives impacted the master mixes differently. Overall, the current study provides insights into the performance of commercial LAMP master mixes, which can be of value for the scientific community to better select appropriate reagents when developing new methods. Full article
(This article belongs to the Special Issue Advances in Foodborne Pathogen Analysis and Detection)
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